diff options
Diffstat (limited to 'reproduce/analysis')
| -rwxr-xr-x | reproduce/analysis/bash/download-multi-try.sh | 85 | ||||
| -rw-r--r-- | reproduce/analysis/config/INPUTS.conf | 2 | ||||
| -rw-r--r-- | reproduce/analysis/config/delete-me-squared-num.conf | 2 | ||||
| -rw-r--r-- | reproduce/analysis/config/metadata.conf | 2 | ||||
| -rw-r--r-- | reproduce/analysis/config/pdf-build.conf | 2 | ||||
| -rw-r--r-- | reproduce/analysis/config/verify-outputs.conf | 2 | ||||
| -rw-r--r-- | reproduce/analysis/make/delete-me.mk | 16 | ||||
| -rw-r--r-- | reproduce/analysis/make/initialize.mk | 167 | ||||
| -rw-r--r-- | reproduce/analysis/make/paper.mk | 79 | ||||
| -rw-r--r-- | reproduce/analysis/make/prepare.mk | 4 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-make.mk | 8 | ||||
| -rw-r--r-- | reproduce/analysis/make/top-prepare.mk | 16 | ||||
| -rw-r--r-- | reproduce/analysis/make/verify.mk | 43 |
13 files changed, 286 insertions, 142 deletions
diff --git a/reproduce/analysis/bash/download-multi-try.sh b/reproduce/analysis/bash/download-multi-try.sh index bea88d5..2df8aab 100755 --- a/reproduce/analysis/bash/download-multi-try.sh +++ b/reproduce/analysis/bash/download-multi-try.sh @@ -31,7 +31,7 @@ # reason, you don't want to use a lock file, set the 'lockfile' name to # 'nolock'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This program is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -90,6 +90,61 @@ urlfile=$(echo "$inurl" | awk -F "/" '{print $NF}') +# Function for downloading +download_func () { + + # Set the arguments. + inurl="$1" + + # During the installation of basic software, the dependencies of the + # downloaders that are installed in Maneage can conflict with the + # downloader that is not yet installed in Maneage. To avoid this, we + # check if the downloader works (with '--version') and remove the + # Maneage library temporarily in case it does not. + lpathorig="" + dprog=$(echo $downloader | awk '{print $1}') + if ! $dprog --version > /dev/null 2> /dev/null; then + echo "NOTE: the segmentation fault is expected, is not a problem" + basedir=$(echo $outname \ + | sed -e's|\/tarballs\/| |' \ + | awk '{print $1}') + libdir=$basedir/installed/lib + lpathorig=$LD_LIBRARY_PATH + lpath=$(echo $LD_LIBRARY_PATH \ + | sed -e's|'$libdir':||') + export LD_LIBRARY_PATH=$lpath + fi + + # Attempt downloading the file. Note that the 'downloader' ends with + # the respective option to specify the output name. For example "wget + # -O" (so 'outname', that comes after it) will be the name of the + # downloaded file. + if [ x"$lockfile" = xnolock ]; then + if ! $downloader $outname $inurl; then rm -f $outname; fi + else + flock "$lockfile" sh -c \ + "if ! $downloader $outname \"$inurl\"; then rm -f $outname; fi" + fi + + # In case the LD_LIBRARY_PATH was changed, set it back to normal. + if ! [ x"$lpathorig" = x ]; then + export LD_LIBRARY_PATH=$lpathorig + fi + + # Some servers return HTTP 4xx/5xx errors as an HTML page with a 200 + # status, so the downloader exits 0 and saves the HTML body to disk. + # Detect this by checking whether the response starts with an HTML tag + # and treat it as a failed download so backup servers will be tried. + if [ -f "$outname" ] \ + && head -c 500 "$outname" 2>/dev/null | grep -qi '<html'; then + rm -f "$outname" + fi +} + + + + + # Try downloading multiple times before crashing. counter=0 maxcounter=10 @@ -119,30 +174,22 @@ while [ ! -f "$outname" ]; do sleep $tstep fi - # Attempt downloading the file. Note that the 'downloader' ends with - # the respective option to specify the output name. For example "wget - # -O" (so 'outname', that comes after it) will be the name of the - # downloaded file. - if [ x"$lockfile" = xnolock ]; then - if ! $downloader $outname $inurl; then rm -f $outname; fi - else - # Try downloading from the requested URL. - flock "$lockfile" sh -c \ - "if ! $downloader $outname \"$inurl\"; then rm -f $outname; fi" - fi + # First attempt at the download. + download_func "$inurl" # If the download failed, try the backup server(s). if [ ! -f "$outname" ]; then if [ x"$backupservers" != x ]; then for bs in $backupservers; do - # Use this backup server. - if [ x"$lockfile" = xnolock ]; then - if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi - else - flock "$lockfile" sh -c \ - "if ! $downloader $outname $bs/$urlfile; then rm -f $outname; fi" - fi + # For Zenodo backup servers, append '?download=1' as well. + bsurl="$bs/$urlfile" + case "$bsurl" in + *zenodo.org*) bsurl="${bsurl}?download=1" ;; + esac + + # Download the file. + download_func "$bsurl" # If the file was downloaded, break out of the loop that # parses over the backup servers. diff --git a/reproduce/analysis/config/INPUTS.conf b/reproduce/analysis/config/INPUTS.conf index 5860806..7373503 100644 --- a/reproduce/analysis/config/INPUTS.conf +++ b/reproduce/analysis/config/INPUTS.conf @@ -105,7 +105,7 @@ # also called '%' (if your local copy of the input dataset and the only # repository names are the same, be sure to set '%' accordingly). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/delete-me-squared-num.conf b/reproduce/analysis/config/delete-me-squared-num.conf index ba8c960..80eb60a 100644 --- a/reproduce/analysis/config/delete-me-squared-num.conf +++ b/reproduce/analysis/config/delete-me-squared-num.conf @@ -1,6 +1,6 @@ # Number of samples in the demonstration analysis (to be deleted). # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/metadata.conf b/reproduce/analysis/config/metadata.conf index 1ab7de1..4c95c2f 100644 --- a/reproduce/analysis/config/metadata.conf +++ b/reproduce/analysis/config/metadata.conf @@ -15,7 +15,7 @@ # and the copyright license name and standard link to the fully copyright # license. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/pdf-build.conf b/reproduce/analysis/config/pdf-build.conf index 7821306..e0400d3 100644 --- a/reproduce/analysis/config/pdf-build.conf +++ b/reproduce/analysis/config/pdf-build.conf @@ -12,7 +12,7 @@ # LaTeX. Otherwise, a notice will just printed that, no PDF will be # created. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/config/verify-outputs.conf b/reproduce/analysis/config/verify-outputs.conf index 031085d..09cca90 100644 --- a/reproduce/analysis/config/verify-outputs.conf +++ b/reproduce/analysis/config/verify-outputs.conf @@ -1,6 +1,6 @@ # To enable verification of output datasets set this variable to 'yes'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # Copying and distribution of this file, with or without modification, are # permitted in any medium without royalty provided the copyright notice and diff --git a/reproduce/analysis/make/delete-me.mk b/reproduce/analysis/make/delete-me.mk index a20abc6..6bba8ba 100644 --- a/reproduce/analysis/make/delete-me.mk +++ b/reproduce/analysis/make/delete-me.mk @@ -1,6 +1,6 @@ # Dummy Makefile to create a random dataset for plotting. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -26,9 +26,9 @@ # and X^2 and draw its plot. # # Note that this dataset is directly read by LaTeX to generate a plot, so -# we need to put it in the $(tex-publish-dir) directory. -dm-squared = $(tex-publish-dir)/squared.txt -$(dm-squared): $(pconfdir)/delete-me-squared-num.conf | $(tex-publish-dir) +# we need to put it in the $(figdir) directory. +dm-squared = $(figdir)/squared.txt +$(dm-squared): $(pconfdir)/delete-me-squared-num.conf | $(figdir) # When the plotted values are re-made, it is necessary to also delete # the TiKZ externalized files so the plot is also re-made by @@ -87,10 +87,10 @@ $(dm-img-pdf): $(dm-histdir)/%.pdf: $(indir)/%.fits | $(dm-histdir) # # For an example plot, we'll show the pixel value histogram also. IMPORTANT # NOTE: because this histogram contains data that is included in a plot, we -# should publish it, so it will go into the $(tex-publish-dir). -dm-img-histogram = $(tex-publish-dir)/wfpc2-histogram.txt -$(dm-img-histogram): $(tex-publish-dir)/%-histogram.txt: $(indir)/%.fits \ - | $(tex-publish-dir) +# should publish it, so it will go into the $(figdir). +dm-img-histogram = $(figdir)/wfpc2-histogram.txt +$(dm-img-histogram): $(figdir)/%-histogram.txt: $(indir)/%.fits \ + | $(figdir) # When the plotted values are re-made, it is necessary to also delete # the TiKZ externalized files so the plot is also re-made. diff --git a/reproduce/analysis/make/initialize.mk b/reproduce/analysis/make/initialize.mk index 92e5eff..250cb25 100644 --- a/reproduce/analysis/make/initialize.mk +++ b/reproduce/analysis/make/initialize.mk @@ -1,6 +1,6 @@ # Project initialization. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -41,7 +41,7 @@ bsdir=$(BDIR)/software # Derived directories (the locks directory can be shared with software # which already has this directory.). texdir = $(badir)/tex -lockdir = $(bsdir)/locks +lockdir = $(badir)/.locks indir = $(badir)/inputs prepdir = $(badir)/prepare mtexdir = $(texdir)/macros @@ -53,6 +53,45 @@ pconfdir = reproduce/analysis/config +# Directories for to-be-published data +# ------------------------------------ +# +# Its good practice (so you don't forget in the last moment!) to have all +# the plot/figure/table data that you ultimately want to publish in a +# single directory. +# +# There are two types of to-publish data in the project. +# +# 1. Those data that also go into your figures/plots (for example to give +# to LateX's PGFPlots package to create the plot internally) should be +# under the '$(texdir)' directory (because other LaTeX producers may +# also need it for example when using './project make dist', or you may +# want to publish the raw data behind the plots, for example see +# Appendix E of [1]). The contents of this directory are also directly +# taken into the tarball. As you see in [1], it is best to keep these +# files in plain-text format. +# +# 2. The data that are not included directly in the paper's figures and +# can be seen as supplements, or a "data release" associated to the +# report. A good place to keep them is under your build-directory +# (since the data may be large). These files can be custom formats like +# FITS files. +# +# RECOMMENDATION: don't put the figure/plot/table number in the names of +# your to-be-published datasets! Given them a descriptive/short name that +# would be clear to anyone who has read the paper. Later, in the caption +# (or paper's tex/appendix), you will put links to the dataset on servers +# like Zenodo (see the "Publication checklist" in 'README-hacking.md'). +# +# [1] https://scixplorer.org/abs/2026A&A...709A.210E +drdir = $(badir)/data-release +figdir = $(texdir)/figures-data +$(figdir) $(drdir):; mkdir $@ + + + + + # Preparation phase # ----------------- # @@ -73,7 +112,7 @@ pconfdir = reproduce/analysis/config ifeq (x$(project-phase),xprepare) $(prepdir):; mkdir $@ else --include $(bsdir)/preparation-done.mk +-include $(badir)/preparation-done.mk ifeq (x$(include-prepare-results),xyes) -include $(prepdir)/*.mk $(prepdir)/*.conf endif @@ -145,6 +184,7 @@ curdir := $(shell echo $$(pwd)) # avoid conflicts with existing TeX Live solutions. Later (in 'paper.mk'), # we are also going to overwrite 'TEXINPUTS' just before 'pdflatex'. .ONESHELL: +export LC_ALL := C export TEXINPUTS := export CCACHE_DISABLE := 1 export PATH := $(installdir)/bin @@ -265,16 +305,8 @@ clean: # executing 'build'. rm -f *.aux *.log *.synctex *.auxlock *.dvi *.out *.run.xml *.bcf -# Delete all the built outputs except the dependency programs. We'll -# use Bash's extended options builtin ('shopt') to enable "extended -# glob" (for listing of files). It allows extended features like -# ignoring the listing of a file with '!()' that we are using -# afterwards. - shopt -s extglob - rm -rf $(texdir)/macros/!(dependencies.tex|dependencies-bib.tex|hardware-parameters.tex) - rm -rf $(badir)/!(tex) $(texdir)/!(macros|$(texbtopdir)) - rm -rf $(texdir)/build/!(tikz) $(texdir)/build/tikz/* - rm -rf $(bsdir)/preparation-done.mk +# Delete the full 'badir' (containing all analysis outputs). + rm -rf $(badir) distclean: clean # Without cleaning the Git hooks, we won't be able to easily commit @@ -285,7 +317,7 @@ distclean: clean # 'rm' program. So for this recipe, we'll use the host system's 'rm', # not our own. $$sys_rm -rf $(BDIR) - $$sys_rm -f .local .build $(pconfdir)/LOCAL.conf + $$sys_rm -f .local .build @@ -329,12 +361,11 @@ $(project-package-contents): paper.pdf | $(texdir) paper.tex > $$dir/paper.tex # Copy ONLY the version-controlled files in 'reproduce' and -# 'tex/src'. This is important because files like 'LOCAL.conf' (in -# 'reproduce/software/config') should not be archived, they contain -# information about the host computer and are irrelevant for -# others. Also some project authors may have temporary files here -# that are not under version control and thus shouldn't be archived -# (although this is bad practice, but that is up to the user). +# 'tex/src'. This is important because the git commit hash goes in +# the tarball name (should correspond to it) and some project authors +# may have temporary files here that are not under version control +# and thus shouldn't be archived (although this is bad practice, but +# that is up to the user). # # To keep the sub-directory structure, we are packaging the files # with Tar, piping it, and unpacking it in the archive directory. So @@ -362,17 +393,20 @@ $(project-package-contents): paper.pdf | $(texdir) rm -rf $$dir/tex/build/build* # If the project has any PDFs in its 'tex/tikz' directory (TiKZ or -# PGFPlots was used to generate them), copy them too. +# PGFPlots was used to generate them), copy them too. Note that in +# the main project source, 'tex/tikz' is just a symbolic link to +# 'tex/build/tikz'. But inside the tarball we do not want to have +# symbolic links and they should be independent. if ls tex/tikz/*.pdf &> /dev/null; then cp tex/tikz/*.pdf $$dir/tex/tikz fi # When submitting to places like arXiv, they will just run LaTeX once -# and won't run 'biber'. So we need to also keep the '.bbl' file into -# the distributing tarball. However, BibLaTeX is particularly -# sensitive to versioning (a '.bbl' file has to be read by the same -# BibLaTeX version that created it). This is hard to do with -# non-up-to-date places like arXiv. Therefore, we thus just copy the +# and won't run 'biber' or 'biblatex'. So we need to also keep the +# '.bbl' file into the distributing tarball. However, BibLaTeX is +# particularly sensitive to versioning (a '.bbl' file has to be read +# by the same BibLaTeX version that created it). This is hard to do +# with non-up-to-date places like arXiv. Therefore, we just copy the # whole of BibLaTeX's source (the version we are using) into the top # tarball directory. In this way, arXiv's LaTeX engine will use the # same BibLaTeX version to interpret the '.bbl' file. TIP: you can @@ -521,7 +555,10 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) # Unrecognized format. *) - echo "Maneage: 'DATABASEAUTHTYPE' format not recognized! Please see the description of this variable in 'reproduce/software/config/LOCAL.conf' for the acceptable values."; exit 1;; + printf "Maneage: 'DATABASEAUTHTYPE' format not recognized! " + printf "Please see the description of this variable in " + printf "'$(bsdir)/config/LOCAL.conf' for the acceptable " + printf "values."; exit 1;; esac fi @@ -597,41 +634,6 @@ $(inputdatasets): $(indir)/%: | $(indir) $(lockdir) -# Directory containing to-be-published datasets -# --------------------------------------------- -# -# Its good practice (so you don't forget in the last moment!) to have all -# the plot/figure/table data that you ultimately want to publish in a -# single directory. -# -# There are two types of to-publish data in the project. -# -# 1. Those data that also go into LaTeX (for example to give to LateX's -# PGFPlots package to create the plot internally) should be under the -# '$(texdir)' directory (because other LaTeX producers may also need it -# for example when using './project make dist', or you may want to -# publish the raw data behind the plots, like: -# https://zenodo.org/record/4291207/files/tools-per-year.txt). The -# contents of this directory are also directly taken into the tarball. -# -# 2. The data that aren't included directly in the LaTeX run of the paper, -# can be seen as supplements. A good place to keep them is under your -# build-directory. -# -# RECOMMENDATION: don't put the figure/plot/table number in the names of -# your to-be-published datasets! Given them a descriptive/short name that -# would be clear to anyone who has read the paper. Later, in the caption -# (or paper's tex/appendix), you will put links to the dataset on servers -# like Zenodo (see the "Publication checklist" in 'README-hacking.md'). -tex-publish-dir = $(texdir)/to-publish -data-publish-dir = $(badir)/data-to-publish -$(tex-publish-dir):; mkdir $@ -$(data-publish-dir):; mkdir $@ - - - - - # Print Copyright statement # ------------------------- # @@ -688,27 +690,40 @@ $(mtexdir)/initialize.tex: # Calculate the latest Maneage commit used to build this project: # - The project may not have the 'maneage' branch (for example # after cloning from a fork that didn't include it!). In this -# case, we'll print a descriptive warning, telling the user what -# should be done (reporting the last merged commit and its date -# is very useful for the future). +# case, if a PDF is to be created, print a descriptive warning, +# telling the user what should be done (reporting the last merged +# commit and its date is very useful for the future). +# - This is not relevant when no PDF is requested because we only +# use this to print the latest Maneage commit as a LaTeX macro. # - The '--dirty' option (used in 'project-commit-hash') isn't # applicable to "commit-ishes" (direct quote from Git's error -# message!). +# message!), so no need to include it here. if git log maneage -1 &> /dev/null; then c=$$(git merge-base HEAD maneage) v=$$(git describe --always --long $$c) d=$$(git show -s --format=%aD $$v | awk '{print $$2, $$3, $$4}') + +# No 'maneage' branch found else - echo - echo "WARNING: no 'maneage' branch found! Without it, the latest merge of " - echo "this project with Maneage can't be reported in the paper (which is bad " - echo "for your readers; that includes yourself in a few years). Please run " - echo "the commands below to fetch the 'maneage' branch from its own server " - echo "and remove this warning (these commands will not affect your project):" - echo " $ git remote add origin-maneage http://git.maneage.org/project.git" - echo " $ git fetch origin-maneage" - echo " $ git branch maneage --track origin-maneage/maneage" - echo + +# Only print a warning if a PDF is to be created. + if [ x$(pdf-build-final) = xyes ]; then + echo + printf "WARNING: no 'maneage' branch found! Without it, " + printf "the latest merge of this project with Maneage can't " + printf "be reported in the paper (which is bad for your " + printf "readers; that includes yourself in a few years). " + printf "Please run the commands below to fetch the " + printf "'maneage' branch from its own server and remove " + printf "this warning (these commands will not affect your " + printf "project):\n" + printf " $ git remote add origin-maneage " + printf "http://git.maneage.org/project.git\n" + printf " $ git fetch origin-maneage\n" + printf " $ git branch maneage --track " + printf "origin-maneage/maneage\n" + echo + fi v="\textcolor{red}{NO-MANEAGE-BRANCH (see printed warning to fix this)}" d="\textcolor{red}{NO-MANEAGE-DATE}" fi diff --git a/reproduce/analysis/make/paper.mk b/reproduce/analysis/make/paper.mk index 66c6859..c218cdd 100644 --- a/reproduce/analysis/make/paper.mk +++ b/reproduce/analysis/make/paper.mk @@ -1,6 +1,6 @@ # Build the final PDF paper/report. # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -18,6 +18,22 @@ + +# Software info in TeX +# -------------------- +# +# The information of the installed software is placed in the +# '.build/software' directory (which the TeX build should not depend +# on). Therefore, we should copy those macros here in the LaTeX build +# directory, so the TeX directory is completely independent from each +# other. +$(mtexdir)/dependencies.tex: $(bsdir)/config/dependencies.tex + cp $(bsdir)/config/*.tex $(mtexdir)/ + + + + + # LaTeX macros for paper # ---------------------- # @@ -39,19 +55,36 @@ # Note that if you don't want the final PDF and just want the processing # and file outputs, you can give any value other than 'yes' to # 'pdf-build-final' in 'reproduce/analysis/config/pdf-build.conf'. -$(mtexdir)/project.tex: $(mtexdir)/verify.tex +$(mtexdir)/project.tex: $(mtexdir)/verify.tex $(mtexdir)/dependencies.tex # If no PDF is requested, or if LaTeX isn't available, don't continue # to building the final PDF. Otherwise, merge all the TeX macros into # one for building the PDF. - @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; then + @if [ -f .local/bin/pdflatex ] && [ x"$(pdf-build-final)" = xyes ]; + then # Put a LaTeX input command for all the necessary macro files. -# 'hardware-parameters.tex' is created in 'configure.sh'. +# Note that 'hardware-parameters.tex' is created in 'configure.sh' +# (which is why it is first in the list). projecttex=$(mtexdir)/project.tex rm -f $$projecttex - for t in $(subst paper,,$(makesrc)) hardware-parameters; do - echo "\input{tex/build/macros/$$t.tex}" >> $$projecttex + for t in hardware-parameters $(subst paper,,$(makesrc)); do + +# Only add the macro file to 'project.tex' if the macro file is +# not empty. Empty macro files are not a bug in Maneage alone: 1) +# the processing of a sub-Makefile may not need to produce any +# written macro for the PDF, and that is perfectly fine. 2) LaTeX +# can also '\input' an empty file. However, it is important for +# for publication servers (like arXiv) that do not allow +# uploading empty files. Therefore, when 'project.tex' contains +# empty files, such severs will not be able compile the PDF +# because the file name is mentioned in 'project.tex', but cannot +# be found in the uploaded files. + tfile=tex/build/macros/$$t.tex + if [ -s $$tfile ]; then + echo "\input{$$tfile}" >> $$projecttex + fi + done # Possibly highlight the '\new' parts of the text. @@ -92,6 +125,23 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex +# TeX build directory +# ------------------- +# +# If built in a group scenario, the TeX build directory must be separate +# for each member (so they can work on their relevant parts of the paper +# without conflicting with each other). +ifeq ($(strip $(maneage_group_name)),) +texbdir:=$(texdir)/build +else +texbdir:=$(texdir)/build-$(shell whoami) +endif +tikzdir:=$(texbdir)/tikz + + + + + # The bibliography # ---------------- # @@ -104,8 +154,8 @@ $(mtexdir)/project.tex: $(mtexdir)/verify.tex # recipe and the 'paper.pdf' recipe. But if 'tex/src/references.tex' hasn't # been modified, we don't want to re-build the bibliography, only the final # PDF. -$(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ - | $(mtexdir)/project.tex +$(texbdir)/paper.bbl: tex/src/references.tex | $(mtexdir)/project.tex + # If '$(mtexdir)/project.tex' is empty, don't build PDF. @macros=$$(cat $(mtexdir)/project.tex) if [ x"$$macros" != x ]; then @@ -130,12 +180,11 @@ $(texbdir)/paper.bbl: tex/src/references.tex $(mtexdir)/dependencies-bib.tex \ # for details. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex biber paper - fi @@ -165,9 +214,9 @@ paper.pdf: $(mtexdir)/project.tex paper.tex $(texbdir)/paper.bbl # option '-shell-escape'. # # We need the modification to 'LD_LIBRARY_PATH' because we do not -# build LaTeX from source and it uses '/bin/sh' (among other -# possible system-wide things). - export LD_LIBRARY_PATH="$(sys_library_sh_path):$$LD_LIBRARY_PATH" +# build LaTeX from source and it (or its packages) may use +# '/bin/sh' (among other possible system-wide things). + export LD_LIBRARY_PATH="$(SYS_LIBRARY_SH_PATH):$$LD_LIBRARY_PATH" pdflatex -shell-escape -halt-on-error "$$p"/paper.tex # Come back to the top project directory and copy the built PDF diff --git a/reproduce/analysis/make/prepare.mk b/reproduce/analysis/make/prepare.mk index 2cc1187..352fd00 100644 --- a/reproduce/analysis/make/prepare.mk +++ b/reproduce/analysis/make/prepare.mk @@ -1,6 +1,6 @@ # Basic preparations, called by './project make'. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -25,7 +25,7 @@ # # We need to remove the 'prepare' word from the list of 'makesrc'. prepare-dep = $(filter-out prepare, $(makesrc)) -$(bsdir)/preparation-done.mk: \ +$(badir)/preparation-done.mk: \ $(foreach s, $(prepare-dep), $(mtexdir)/$(s).tex) # If you need to add preparations (mainly automatically generated diff --git a/reproduce/analysis/make/top-make.mk b/reproduce/analysis/make/top-make.mk index 2689e64..7286ca6 100644 --- a/reproduce/analysis/make/top-make.mk +++ b/reproduce/analysis/make/top-make.mk @@ -1,6 +1,6 @@ # Top-level Makefile (first to be loaded). # -# Copyright (C) 2018-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2018-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -19,9 +19,9 @@ -# Load the local configuration (created after running -# './project configure'). -include reproduce/software/config/LOCAL.conf +# Load the local configuration (created after running './project +# configure'). +include .build/software/config/LOCAL.conf diff --git a/reproduce/analysis/make/top-prepare.mk b/reproduce/analysis/make/top-prepare.mk index 7d92d72..913a062 100644 --- a/reproduce/analysis/make/top-prepare.mk +++ b/reproduce/analysis/make/top-prepare.mk @@ -4,7 +4,7 @@ # are not included here. Please see that file for thorough comments on each # step. # -# Copyright (C) 2019-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2019-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -23,9 +23,9 @@ -# Load the local configuration (created after running -# './project configure'). -include reproduce/software/config/LOCAL.conf +# Load the local configuration (created after running './project +# configure'). +include .build/software/config/LOCAL.conf @@ -36,16 +36,16 @@ include reproduce/software/config/LOCAL.conf # # See 'top-make.mk' for complete explanation. ifeq (x$(maneage_group_name),x$(GROUP-NAME)) -all: $(BDIR)/software/preparation-done.mk +all: $(BDIR)/analysis/preparation-done.mk @echo "Project preparation is complete."; else all: @if [ "x$(GROUP-NAME)" = x ]; then \ echo "Project is NOT configured for groups, please run"; \ - echo " $$ ./project prepare"; \ + echo " $$ ./project configure"; \ else \ echo "Project is configured for groups, please run"; \ - echo " $$ ./project prepare --group=$(GROUP-NAME) -j8"; \ + echo " $$ ./project configure --group=$(GROUP-NAME) -j8"; \ fi exit 1 endif @@ -61,7 +61,7 @@ endif # # To ensure that 'prepare' and 'make' have the same basic definitions and # environment and that all 'downloads' are managed in one place, both -# './project prepare' and './project make' will first read 'initialize.mk' +# './project configure' and './project make' will first read 'initialize.mk' # and 'downloads.mk'. makesrc = initialize \ prepare diff --git a/reproduce/analysis/make/verify.mk b/reproduce/analysis/make/verify.mk index c74f8ca..91c4b77 100644 --- a/reproduce/analysis/make/verify.mk +++ b/reproduce/analysis/make/verify.mk @@ -1,6 +1,6 @@ # Verify the project outputs before building the paper. # -# Copyright (C) 2020-2025 Mohammad Akhlaghi <mohammad@akhlaghi.org> +# Copyright (C) 2020-2026 Mohammad Akhlaghi <mohammad@akhlaghi.org> # # This Makefile is free software: you can redistribute it and/or modify # it under the terms of the GNU General Public License as published by @@ -138,11 +138,44 @@ $(mtexdir)/verify.tex: $(foreach s, $(verify-dep), $(mtexdir)/$(s).tex) # Verify TeX macros (the values that go into the PDF text). for m in $(verify-check); do - file=$(mtexdir)/$$m.tex - if [ $$m == delete-me ]; then s=711e2f7fa1f16ecbeeb3df6bcb4ec705 - else echo; echo "'$$m' not recognized."; exit 1 + +# Set the macro file name, make sure it exists (the user may have +# forgot to create it in the respective sub-Makefile). + tfile=$(mtexdir)/$$m.tex + if ! [ -f $$tfile ]; then + printf "$$tfile: ERROR: does not exist! If you do not " + printf "(currently) plan macros to be added to the final " + printf "PDF from that sub-Makefile, do the following to " + printf "avoid this error: put a 'touch \$$@' as the recipe " + printf "of the '\$$(mtexdir)/$$m.tex' target (at the bottom " + printf "of 'reproduce/analysis/make/$$m.mk'). If you later " + printf "decide to define macros there, simply replace the " + printf "temporary 'touch \$$@' command with the command(s) " + printf "to prepare/write the macro (see 'initialize.mk' " + printf "as an example)\n"; + exit 1 fi - $(call verify-txt-no-comments-no-space, $$file, $$s, $@.tmp) + +# Check the hash for this file and verify it. + case $$m in + delete-me) s=711e2f7fa1f16ecbeeb3df6bcb4ec705;; + *) # This file's hash is not in the list above. + +# If the file is empty, we can skip it (with the 'continue' +# command). Otherwise, the user should be informed with an +# error. + if [ -s $$tfile ]; then + printf "$$tfile: ERROR: please add the hash of this " + printf "macro file to the list of hashes above this " + printf "error message (in " + printf "'reproduce/analysis/make/verify.mk')\n"; exit 1 + else + continue + fi + ;; + esac + $(call verify-txt-no-comments-no-space, $$tfile, $$s, $@.tmp) + done # Move temporary file to final target. |